1.. He views prayer as ... It is a working together with God.

Why 'a working"? Could it be 'an instance of working'?

2. A "good morning" in the morning can lift one's spirit up.

This sentence I made up -- can the article "a" mean "an instance of saying "good morning"?I am confused because because with the word like "injustice" it is easy to conceive what an "instance" might be referring to: probably refers to an instance of injustice, which bring up an image of improper treatment -- and which, to me, perceiving an instance of it is pretty clear; but with "a 'good morning'" -- it is hard to conceive what an instance of it might be, might be an instance of saying "good morning"? Confused. Help.

3. He offers them ... nurishment for soul and body.

Why no articles in front of "soul" and "body"? Can a person use any word as an uncountable as he seems to fit? I think not. But I hve seen these words without the artcles in writings; so, if they are seen in writings often, should I take the use of them as good?

Mother and daughter had come to the big city.

Why no articles before "daughter" and "mother"? Is a person noting them as roles? Can this kind of use be valid in an scholarly writing?

Thank you.
These are interesting questions. Here are my non-expert thoughts, but others may have different views.

1. He views prayer as ... It is a working together with God.

To me, "a prayer ... is a working together with God" would be talking about an individual instance of working together (lasting just for that one prayer), while "prayer ... is a working together with God" (as you have here) suggests more an ongoing working relationship. Lots of prayers, lots of working together -- that could be viewed as a series of acts of working together (one per prayer), but is more likely just a general persistent state that is topped up by prayers but doesn't stop and start with each prayer.

2. A "good morning" in the morning can lift one's spirit up.

Yes, the article "a" means "an instance of", but it's ambiguous whether it's an instance of saying or of hearing.

3. He offers them ... nourishment for soul and body.

Not all countable nouns can be turned into uncountable nouns. The ones that can generally become abstracted from an individual instance (countable) to a general concept (uncountable), as in "we're fighting an injustice" versus "we're fighting injustice". I suppose it's just about possible for the words "body" and "soul" to be individually abstracted to uncountable nouns ("nourishment for body"), but this is fairly rare, and to me risks looking like a typo or grammatical error.

The case of "body and soul" is different: "body and soul" acts as a single unit, and that's the uncountable noun. Think of it as "bodyandsoul" (though obviously it's never written like that). So, "body and soul" is a kind of abstraction of an individual body and its accompanying soul to the general concept. Confusingly, though, this abstraction can still refer to a single body/soul (as well as to bodies/souls in general), as in "I eat simply but I keep body and soul together" (rather than "my body and soul together"). My guess is that this is a sort of "distancing" that removes the need to contemplate an individual physical body and the possible actual existence of a soul.

4. Mother and daughter had come to the big city.

This use is IMO fine in all types of writing, but to me it tends to personalise the individuals -- put us "closer" to them, if you like -- which might be inappropriate in some contexts. The roles are clearly being noted, but that by itself doesn't seem to explain the lack of articles. Neither does it seem to be in any sense an abstraction of the concept of mother and daughter. My guess is that grammatically "mother" and "daughter" substitute for the people's names (which obviously would not need articles).
Thank you, Mr. Wordy. You are not just wordy -- you are wisely wordy.